Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evidence for rRNA 2'-O-methylation plasticity: control of intrinsic translational capabilities of human ribosomes

ABSTRACT: Ribosomal RNAs (rRNAs) are main effectors of mRNA decoding, peptide-bond formation and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and display a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin (FBL) in human cells. Using RiboMethSeq, a non-biased quantitative mapping of 2'-O-Me, we identified a repertoire of 2'-O-Me sites subjected to variation and demonstrate that functional domains of ribosomes are targets of 2'-O-Me plasticity. Using the cricket paralysis virus (CrPV) IRES element, as a model, coupled to in vitro translation, we show that the intrinsic capability of ribosomes to translate mRNAs is modulated through 2'-O-Me pattern and not by non-ribosomal actors of the translational machinery. Our results establish rRNA 2'-O-methylation plasticity as a mechanism providing functional specificity to human ribosomes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE105248 | GEO | 2018/01/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

p26 condensates from Pea enation mosaic virus 2 sequester ribosomal components and suppress translation

Project description:The p26 movement protein of Pea enation mosaic virus 2 (PEMV2) interacts with the 2'-O-methyltransferase fibrillarin within nuclear and cytoplasmic condensates. This study analyzed global 2'-O-methylation patterns in PEMV2-infected Nicotiana benthamiana using RiboMethSeq, focusing on ribosomal RNAs (rRNAs). The aim was to assess whether PEMV2 disrupts rRNA 2'-O-methylation to interfere with host translation or ribosome assembly.

2024-11-18 | GSE275487 | GEO

The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [ribomethseq_primary_samples]

Project description:Eukaryotic ribosomal RNA carries diverse posttranscriptional modifications, the function of which are mostly unexplored. The evolutionarily conserved 2’-O-methylation (2’-O-Me) occurs at more than 100 sites and is essential for ribosome biogenesis. Plasticity of 2´-O-Me in ribosomes and its functional consequences in human disease remain to be elucidated. We performed RiboMethSeq to estabolish the full rRNA 2’-O-Me landscape (ribomethylome) in human acute myeloid leukemia (AML) through profiling 94 patient samples as well as 21 normal hematopoietic samples of 5 different lineages. The gene expression in the same samples was determined by RNA-Seq. We found that higher 2’-O-methylation on exterior dynamic sites associated with leukemia stem cell (LSC) signatures.

2022-11-23 | GSE184727 | GEO

The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [mRNA_primary_samples]

2022-11-23 | GSE184722 | GEO

The RNA-binding protein Hfq is important for ribosome biogenesis and affects translation fidelity

Project description:Ribosome biogenesis is a complex and intricate process involving multiple factors. A plethora of auxiliary proteins assist the correct assembly of rRNA and ribosomal proteins into mature ribosomes. Defects in this process cause dysfunctional ribosomes which may alter protein synthesis and impair cell fitness. Despite its importance, yet we are lacking mechanistic details of ribosome biogenesis. Here we show that the widely-conserved RNA chaperone Hfq, which is an important post-transcriptional regulator in sRNA-mRNA basepairing in Escherichia coli, plays a critical role in rRNA processing and consequently ribosome assembly. Hfq binds the 17S rRNA precursor and facilitates its correct processing and folding to mature 16S rRNA. Strikingly, Hfq depletion decreases the pool of mature 70S ribosomes. Mutations in residues located in the distal face of Hfq render reduced ribosome levels in contrast to mutations in the proximal and rim surfaces which govern interactions with the sRNAs. Our results indicate that the described Hfq-dependent regulation of ribosomes is independent of its function as sRNA-regulator. Furthermore, we observed that inactivation of Hfq compromises translation efficiency and fidelity, both features of aberrantly assembled ribosomes. Our work expands the functions of Hfq beyond its function in small RNA-mediated regulation and unveil a novel role of Hfq as crucial auxiliary factor in ribosome biogenesis and translation.

2018-04-18 | GSE100373 | GEO

The dynamic rRNA ribomethylome drives stemness in acute myeloid leukemia [mRNA_FBL_KD]

Project description:Eukaryotic ribosomal RNA carries diverse posttranscriptional modifications, the function of which are mostly unexplored. The evolutionarily conserved 2’-O-methylation (2’-O-Me) occurs at more than 100 sites and is essential for ribosome biogenesis. Plasticity of 2´-O-Me in ribosomes and its functional consequences in human disease remain to be elucidated. The effect of rRNA 2’-O-Me on protein translation was investigated by nascent proteomcis analysis coupled with RNA-Seq in human leukemia cell line Kasumi-1 with and without knockdown of 2´-O-methyltransferase FBL.

2022-11-23 | GSE184721 | GEO

R-protein composition of budding yeast PTC deficient 80S ribosomes

Project description:Ribosomal RNA modifications are introduced during ribosome assembly by snoRNA and stand-alone modification enzyme based mechanisms in budding yeast. Lack of individual modifications in rRNA has a minor effect on yeast growth, ribosome biogenesis, and translation, which has complicated the definition of the biological function of rRNA modifications. We have constructed a S.cerevisiae strain lacking 7 25S rRNA modifications (Ψ2826, Um2921, Gm2619, m5C2870, Ψ2880, Um2724 and Gm2922)in peptidyl-transferase center. This strain exhibits severely compromised growth at 30°C, reduced level of global translation and actively translating ribosomes and cold sensitivity. Ribosomal protein composition of the mature 80S ribosomes was analyzed by SILAC based qMS approach. We have found that absence of PTC modifications around PTC does not affect significantly r-protein content of 80S ribosomes.

2024-06-23 | PXD051211 | Pride

Effect of rRNA methylation defect on protein composition of human ribosomes

Project description:Ribosomal RNAs (rRNAs) are main effectors of mRNA decoding, peptide-bond formation and ribosome dynamics during translation. Ribose 2'-O-methylation is the most abundant rRNA chemical modification, and display a complex pattern in rRNA. We globally challenged rRNA 2'-O-Me by inhibiting the rRNA methyl-transferase fibrillarin (FBL) in human cells. Since FBL participates in rRNA processing, we wonder if FBL knockdown could alter the assembly of ribosomes.

2018-04-09 | PXD007244 | Pride

Divergent rRNAs as regulators of gene expression at the ribosome level

Project description:It is generally assumed that each organism has evolved to possess a unique ribosomal RNA (rRNA) species optimal for its physiological needs. However, some organisms express divergent rRNAs, the functional roles of which remain unknown. Here, we show that ribosomes containing the most variable rRNAs, encoded by the rrnI operon (herein designated I-ribosomes), direct the preferential translation of a subset of mRNAs in Vibrio vulnificus, enabling the rapid adaptation of bacteria to temperature and nutrient shifts. In addition, genetic and functional analyses of I-ribosomes and target mRNAs suggest that both I-ribosomal subunits are required for the preferential translation of specific mRNAs, the Shine-Dalgarno sequences of which do not play a critical role in I-ribosome binding. This study identifies genome-encoded divergent rRNAs as regulators of gene expression at the ribosome level, providing an additional level of regulation of gene expression in bacteria in response to environmental changes.

2018-11-27 | GSE111991 | GEO

R-proteins in modification deficient ribosomes - free 50S subunits

Project description:Ribosomal RNA modifications are introduced by specific enzymes during ribosome assembly in bacteria. Deletion of individual modification enzymes has a minor effect on bacterial growth, ribosome biogenesis, and translation, which has complicated the definition of the function of the enzymes and their products. We have constructed an E. coli strain lacking 10 genes encoding enzymes that modify 23S rRNA around the peptidyl-transferase center. This strain exhibits severely compromised growth and ribosome assembly, especially at lower temperatures. Ribosomal protein composition of the mature 50S ribosomes and free 50S subunits was analyzed by SILAC based qMS approach. We have found that absence of 23S rRNA modifications around PTC does not affect significantly r-protein content of incompletely assembled 50S or mature 50S ribosomes.

2024-03-15 | PXD047376 | Pride

R-proteins in modification deficient ribosomes - dissociated 50S subunits from 70S

2024-03-15 | PXD047588 | Pride